[Biopython-dev] Bio/SearchIO/BlastIO/blast_xml.py output under Python 2.7.4

Peter Cock p.j.a.cock at googlemail.com
Mon Apr 8 17:08:57 UTC 2013

On Mon, Apr 8, 2013 at 6:02 PM, Wibowo Arindrarto <bow at bow.web.id> wrote:
> Hi Peter, everyone,
> This is reproducible in my machine (which just happen to update its default
> Python2.x to 2.7.4 actually). Looks like they changed the underlying SAX XML
> writer (xml.sax.saxutils.XMLGenerator ~ which the SearchIO blast_xml writer
> subclasses). The new write() method calls the io.TextIOWrapper.write()
> function, which expects unicode only.
> See the comparison here:
> Python2.7.3
> (http://hg.python.org/cpython/file/70274d53c1dd/Lib/xml/sax/saxutils.py#l84)
> vs Python2.7.4
> (http://hg.python.org/cpython/file/026ee0057e2d/Lib/xml/sax/saxutils.py#l109).
> Also, here's the io module doc page for reference:
> http://docs.python.org/2/library/io.html
> I'll write up a Python <=2.7.3-compatible patch to fix this soon, if
> everybody's ok with it :).
> Cheers,
> Bow

Sounds good - with the combination of TravisCI and the buildbot we should
have the major platforms covered.



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